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Transcription, Genetic

  • 1.
    Lim A, Li Y, Lopez-Lastra S, Stadhouders R, Paul F, Casrouge A, Serafini N, Puel A, Bustamante J, Surace L, Masse-Ranson G, David E, Strick-Marchand H, Le Bourhis L, Cocchi R, Topazio D, Graziano P, Muscarella L, Rogge L, Norel X, Sallenave J-M, Allez M, Graf T, Hendriks R, Casanova J-L, Amit I, Yssel H, Di Santo J. Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation. Cell. 2017;168(6):1086–1100.e10. PMID: 28283063
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    Levo M, Raimundo J, Bing X, Sisco Z, Batut P, Ryabichko S, Gregor T, Levine M. Transcriptional coupling of distant regulatory genes in living embryos. Nature. 2022;605(7911):754–760. PMCID: PMC9886134
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    Koch M, Black M, Han E, Shaevitz J, Gitai Z. distinguishes surfaces by stiffness using retraction of type IV pili. Proc Natl Acad Sci U S A. 2022;119(20):e2119434119. PMCID: PMC9171759
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    Batut P, Bing X, Sisco Z, Raimundo J, Levo M, Levine M. Genome organization controls transcriptional dynamics during development. Science. 2022;375(6580):566–570. PMID: 35113722
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    Miangolarra M, Li S, Joanny J-F, Wingreen N, Castellana M. Steric interactions and out-of-equilibrium processes control the internal organization of bacteria. Proc Natl Acad Sci U S A. 2021;118(43). PMCID: PMC8639350
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    Lemma A, Brynildsen M. Toxin Induction or Inhibition of Transcription or Translation Posttreatment Increases Persistence to Fluoroquinolones. mBio. 2021;12(4):e0198321. PMCID: PMC8406316
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  • 1.
    Ing-Simmons E, Vaid R, Bing X, Levine M, Mannervik M, Vaquerizas J. Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning. Nat Genet. 2021;53(4):487–499. PMCID: PMC8035076
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  • 1.
    Lim B, Levine M. Enhancer-promoter communication: hubs or loops?. Curr Opin Genet Dev. 2021;67:5–9. PMCID: PMC8653970
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  • 1.
    Li A, Okada B, Rosen P, Seyedsayamdost M. Piperacillin triggers virulence factor biosynthesis via the oxidative stress response in . Proc Natl Acad Sci U S A. 2021;118(26). PMCID: PMC8256049
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  • 1.
    Zhao E, Lalwani M, Chen J-M, Orillac P, Toettcher J, Avalos J. Optogenetic Amplification Circuits for Light-Induced Metabolic Control. ACS Synth Biol. 2021;10(5):1143–1154. PMCID: PMC8721662
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  • 1.
    Treen N, Shimobayashi S, Eeftens J, Brangwynne C, Levine M. Properties of repression condensates in living Ciona embryos. Nat Commun. 2021;12(1):1561. PMCID: PMC7946874
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  • 1.
    Shidlovskii Y, Bylino O, Shaposhnikov A, Kachaev Z, Lebedeva L, Kolesnik V, Amendola D, De Simone G, Formicola N, Schedl P, Digilio F, Giordano E. Subunits of the PBAP Chromatin Remodeler Are Capable of Mediating Enhancer-Driven Transcription in . Int J Mol Sci. 2021;22(6). PMCID: PMC7999800
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  • 1.
    Colonnetta M, Lym L, Wilkins L, Kappes G, Castro E, Ryder P, Schedl P, Lerit D, Deshpande G. Antagonism between and Torso receptor regulates transcriptional quiescence underlying germline/soma distinction. Elife. 2021;10. PMCID: PMC7843132
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  • 1.
    Heimbucher T, Hog J, Gupta P, Murphy C. PQM-1 controls hypoxic survival via regulation of lipid metabolism. Nat Commun. 2020;11(1):4627. PMCID: PMC7532158
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  • 1.
    Ravindran P, Wilson M, Jena S, Toettcher J. Engineering combinatorial and dynamic decoders using synthetic immediate-early genes. Commun Biol. 2020;3(1):436. PMCID: PMC7426417
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  • 1.
    Chen H, Gregor T. Using RNA Tags for Multicolor Live Imaging of Chromatin Loci and Transcription in Drosophila Embryos. Methods Mol Biol. 2020;2166:373–384. PMCID: PMC8130451
    Reference Link
  • 1.
    Cao W, Kabelitz S, Gupta M, Yeung E, Lin S, Rammelt C, Ihling C, Pekovic F, Low T, Siddiqui N, Cheng M, Angers S, Smibert C, Wühr M, Wahle E, Lipshitz H. Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition. Cell Rep. 2020;31(12):107783. PMCID: PMC7372737
    Reference Link
  • 1.
    Richter F, Morton S, Kim S, Kitaygorodsky A, Wasson L, Chen K, Zhou J, Qi H, Patel N, DePalma S, Parfenov M, Homsy J, Gorham J, Manheimer K, Velinder M, Farrell A, Marth G, Schadt E, Kaltman J, Newburger J, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter G, Bernstein D, Chung W, Srivastava D, Tristani-Firouzi M, Troyanskaya O, Dickel D, Shen Y, Seidman J, Seidman C, Gelb B. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet. 2020;52(8):769–777. PMCID: PMC7415662
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  • 1.
    Rath S, Prangley E, Donovan J, Demarest K, Wingreen N, Meir Y, Korennykh A. Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in the dsRNA Response. Mol Cell. 2019;75(6):1218–1228.e6. PMCID: PMC6754276
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  • 1.
    Adolfsen K, Chou W, Brynildsen M. Transcriptional Regulation Contributes to Prioritized Detoxification of Hydrogen Peroxide over Nitric Oxide. J Bacteriol. 2019;201(14). PMCID: PMC6597392
    Reference Link
  • 1.
    Zhou J, Park C, Theesfeld C, Wong A, Yuan Y, Scheckel C, Fak J, Funk J, Yao K, Tajima Y, Packer A, Darnell R, Troyanskaya O. Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. Nat Genet. 2019;51(6):973–980. PMCID: PMC6758908
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  • 1.
    Braffman N, Piscotta F, Hauver J, Campbell E, Link J, Darst S. Structural mechanism of transcription inhibition by lasso peptides microcin J25 and capistruin. Proc Natl Acad Sci U S A. 2019;116(4):1273–1278. PMCID: PMC6347699
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  • 1.
    Lebedeva L, Yakovlev K, Kozlov E, Schedl P, Deshpande G, Shidlovskii Y. Transcriptional quiescence in primordial germ cells. Crit Rev Biochem Mol Biol. 2018;53(6):579–595. PMCID: PMC8729227
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  • 1.
    Gilbertson S, Federspiel J, Hartenian E, Cristea I, Glaunsinger B. Changes in mRNA abundance drive shuttling of RNA binding proteins, linking cytoplasmic RNA degradation to transcription. Elife. 2018;7. PMCID: PMC6203436
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    Sigoillot F, Lyman S, Huckins J, Adamson B, Chung E, Quattrochi B, King R. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. Nat Methods. 2012;9(4):363–6. PMCID: PMC3482495
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    Gilbert L, Horlbeck M, Adamson B, Villalta J, Chen Y, Whitehead E, Guimaraes C, Panning B, Ploegh H, Bassik M, Qi L, Kampmann M, Weissman J. Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell. 2014;159(3):647–61. PMCID: PMC4253859
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    Adamson B, Norman T, Jost M, Cho M, Nuñez J, Chen Y, Villalta J, Gilbert L, Horlbeck M, Hein M, Pak R, Gray A, Gross C, Dixit A, Parnas O, Regev A iv, Weissman J. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell. 2016;167(7):1867–1882.e21. PMCID: PMC5315571
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  • 1.
    Patel A, Shvartsman S. Outstanding questions in developmental ERK signaling. Development. 2018;145(14). PMCID: PMC6078328
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  • 1.
    Painter H, Chung N, Sebastian A, Albert I, Storey J, Llinás M. Genome-wide real-time in vivo transcriptional dynamics during Plasmodium falciparum blood-stage development. Nat Commun. 2018;9(1):2656. PMCID: PMC6037754
    Reference Link
  • 1.
    Chen H, Levo M, Barinov L, Fujioka M, Jaynes J, Gregor T. Dynamic interplay between enhancer-promoter topology and gene activity. Nat Genet. 2018;50(9):1296–1303. PMCID: PMC6119122
    Reference Link
  • 1.
    vonHoldt B, Ji S, Aardema M, Stahler D, Udell M, Sinsheimer J. Activity of Genes with Functions in Human Williams-Beuren Syndrome Is Impacted by Mobile Element Insertions in the Gray Wolf Genome. Genome Biol Evol. 2018;10(6):1546–1553. PMCID: PMC6007319
    Reference Link
  • 1.
    Ding Q, Nimgaonkar I, Archer N, Bram Y, Heller B, Schwartz R, Ploss A. Identification of the Intragenomic Promoter Controlling Hepatitis E Virus Subgenomic RNA Transcription. mBio. 2018;9(3). PMCID: PMC5941075
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  • 1.
    Wilson M, Ravindran P, Lim W, Toettcher J. Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. Mol Cell. 2017;67(5):757–769.e5. PMCID: PMC5591080
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  • 1.
    Johnson H, Goyal Y, Pannucci N, Schüpbach T, Shvartsman S, Toettcher J. The Spatiotemporal Limits of Developmental Erk Signaling. Dev Cell. 2017;40(2):185–192. PMCID: PMC5289754
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  • 1.
    Frederick D, Loro E, Liu L, Davila A, Chellappa K, Silverman I, Quinn W, Gosai S, Tichy E, Davis J, Mourkioti F, Gregory B, Dellinger R, Redpath P, Migaud M, Nakamaru-Ogiso E, Rabinowitz J, Khurana T, Baur J. Loss of NAD Homeostasis Leads to Progressive and Reversible Degeneration of Skeletal Muscle. Cell Metab. 2016;24(2):269–82. PMCID: PMC4985182
    Reference Link
  • 1.
    Papazyan R, Sun Z, Kim Y, Titchenell P, Hill D, Lu W, Damle M, Wan M, Zhang Y, Briggs E, Rabinowitz J, Lazar M. Physiological Suppression of Lipotoxic Liver Damage by Complementary Actions of HDAC3 and SCAP/SREBP. Cell Metab. 2016;24(6):863–874. PMCID: PMC5159233
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  • 1.
    Ding Q, von Schaewen M, Hrebikova G, Heller B, Sandmann L, Plaas M, Ploss A. Mice Expressing Minimally Humanized CD81 and Occludin Genes Support Hepatitis C Virus Uptake In Vivo. J Virol. 2017;91(4). PMCID: PMC5286898
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  • 1.
    Robinson J, Brynildsen M. An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli. Metab Eng. 2015;31:22–34. PMID: 26112956
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  • 1.
    Fukaya T, Lim B, Levine M. Enhancer Control of Transcriptional Bursting. Cell. 2016;166(2):358–368. PMCID: PMC4970759
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  • 1.
    Castellana M, Li S, Wingreen N. Spatial organization of bacterial transcription and translation. Proc Natl Acad Sci U S A. 2016;113(33):9286–91. PMCID: PMC4995950
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  • 1.
    Momen-Roknabadi A, Di Talia S, Wieschaus E. Transcriptional Timers Regulating Mitosis in Early Drosophila Embryos. Cell Rep. 2016;16(11):2793–2801. PMCID: PMC5386176
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  • 1.
    Beh L, Müller M, Muir T, Kaplan N, Landweber L. DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome. Genome Res. 2015;25(11):1727–38. PMCID: PMC4617968
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  • 1.
    Digianantonio K, Hecht M. A protein constructed de novo enables cell growth by altering gene regulation. Proc Natl Acad Sci U S A. 2016;113(9):2400–5. PMCID: PMC4780649
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  • 1.
    Mok W, Park J, Rabinowitz J, Brynildsen M. RNA Futile Cycling in Model Persisters Derived from MazF Accumulation. mBio. 2015;6(6):e01588–15. PMCID: PMC4659464
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  • 1.
    Berry J, Weber S, Vaidya N, Haataja M, Brangwynne C. RNA transcription modulates phase transition-driven nuclear body assembly. Proc Natl Acad Sci U S A. 2015;112(38):E5237–45. PMCID: PMC4586886
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  • 1.
    Little S, Sinsimer K, Lee J, Wieschaus E, Gavis E. Independent and coordinate trafficking of single Drosophila germ plasm mRNAs. Nat Cell Biol. 2015;17(5):558–68. PMCID: PMC4417036
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  • 1.
    Levine M, Cattoglio C, Tjian R. Looping back to leap forward: transcription enters a new era. Cell. 2014;157(1):13–25. PMCID: PMC4059561
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  • 1.
    Bothma J, Garcia H, Esposito E, Schlissel G, Gregor T, Levine M. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proc Natl Acad Sci U S A. 2014;111(29):10598–603. PMCID: PMC4115566
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  • 1.
    Erokhin M, Elizar’ev P, Parshikov A, Schedl P, Georgiev P, Chetverina D. Transcriptional read-through is not sufficient to induce an epigenetic switch in the silencing activity of Polycomb response elements. Proc Natl Acad Sci U S A. 2015;112(48):14930–5. PMCID: PMC4672805
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  • 1.
    Falahati H, Pelham-Webb B, Blythe S, Wieschaus E. Nucleation by rRNA Dictates the Precision of Nucleolus Assembly. Curr Biol. 2016;26(3):277–85. PMCID: PMC5866055
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